Trying to get my head round this if anyone can help ?

I've created a gametype as 5flag CTF with shotguns, 30min gametime, it works ok with classic maps - but when it's loaded with some custom maps eg. delta_ruined, the game ends after just 1 flag is scored ? Tried it on the LAN and also my server with the same result. I've rechecked the gametype and 5 flags is definitely set, but the gametime has reset back to the default no time limit. If I edit and change it to a specific time and save it again, then when I recheck it always resets again.
Is this something with the map that's overriding the gametype settings ? I'm also using sapp, so wondered if it's possible to do something to fix this using that ? No idea how though.

Any ideas ?
Thanks :)